1. The Transcriptional Landscape of the Mammalian Genome
RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium

2. The FANTOM project
Solving biological questions using bioinformatics, and technology
FANTOM1-Production of full length sequence mouse DNA. Design of functional annotation of cDNA.
FANTOM2-Assignment of annotations and bp determination of full length mouse cDNA.
FANTOM3- Utilization of CAGE uncovering more info on the transcriptome.
Functional annotation referring to: attributes such as molecular function, biological process and cellular component -GO terms (Gene Ontology)

3. Background
At this point, whole genome sequencing was impractical and expensive
NGS~2008
GSC(genome signature cloning)/ GIC ditag- full cDNA cloning with the cleavage of internal sequences
Transcriptional landscape- pattern of transcriptional control signals, and the transcripts they generate
Transcriptional units (TU)
Transcriptional framework (TK)
GSC(genome signature cloning)/ GIC ditag- full cDNA cloning with the cleavage of internal sequences, leaving the 5’ and 3’ end of cDNA which are then amplified then cloned

4. Background
Expressed sequence tags (EST)- Short (200–800 nucleotide bases in length), unedited, randomly selected single-pass sequence reads derived from cDNA libraries.
*Sampling bias-rare transcripts?
EST-The 5’ and 3’ UTRs of eukaryotic mRNA have been experimentally shown to contain sequence elements essential for gene regulation, expression and translation [16]. In this context, EST data has proven to be important for mining UTRs as both 50 and 30 ESTs contain significant sections of the UTRs along with protein coding regions.

5. Methods CAGE- cap analysis gene expression
Capture of 5’ cap using a linker
Cleavage
Amplification
Concatenation+linkers
Cloning into vector

6. 36166 protein isoforms identified between FANTOM 1-3 and external sources
FANTOM 3 added proteins of which mapped to new transcriptional frameworks

7. CAGE tags align to transcriptional start sites

8. Prediction of transcript length distribution in the genome
Transcriptional forest predicted to collapse as depth of coverage increase

9. Cage tags in first exon show preference for 5’ end
Cage tags in last exon show preference for 3’ end
Antisense transcription

10. Promoter sequences are highly conserved across mouse and humans, more so in nc promoters.
* Compared to chicken also but much less alignment, expected since different class

11. Significance
CAGE method allowed for identification of promoter regions, gave insight into transcriptome
Tags binding to 3’ region- antisense transcription
Non coding RNAs appear to be highly conserved in promoter regions, only 40% of known ncRNAs were isolated and sequenced
Establishment of databases for cDNA annotation, expression, and analysis
Antisense strands seem to participate in regulatory mechanisms which influences genes

12. Conclusions
CAGE revealed transcriptional initiation and termination sites
63% of the genome is transcribed as RNA in regions called transcriptional forests
Transcriptional deserts collapse as more TUs are discovered
The mammalian transcriptome is highly complex, transcripts overlap

13. Future Studies Mega transcripts(~2.2Mb)- new cloning technology needed
Look at nuclear RNA
Laid groundwork for comparative transcriptional studies between mammals
Function of ncRNDA?
FANTOM4, FANTOM5
The identification of mega transcripts gave insight into the future direction of cloning technology
ncRNAs are highly conserved across all species even those evolutionary distantly related, especially their promoters; when compared to promoters of coding RNA. What is their function?

14. References What/Who is FANTOM? http://fantom.gsc.riken.jp/ EST
pressed_Sequence_Tag_EST_Analysis/links/00b7d52fa880e pdf
Tag methods

15. Further Reading Anti sense RNA
Long noncoding RNAs: functional surprises from the RNA world
Tiny RNAs associated with transcription start sites in animals (FANTOM 4)